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mtekman

33 karma · joined July 30, 2021

Senior Bioinformatician and Single-cell RNA-seq Specialist.

* CV: https://drive.google.com/file/d/1Pmd-jwZjUIAif0qPCyjs6Xk5URK7A9cN

Experienced in data analysis, machine learning, teaching, full stack web dev, self-hosted services, and various hobby projects such as drone hacking, home automation, and bots.

Main Languages: R, JavaScript, Python, C++, Common Lisp, SQL

Reproducibility: Docker, Conda, Biocontainers, and Guix

Pipelines: Galaxy, Nextflow, Snakemake

Management: Teaching, lecturing, mentoring, countless workshops, matrix management role.

I was part of the core Freiburg Galaxy scRNA-seq founding team, wrote tons of tools and trainings.

* Gitlab: https://gitlab.com/mtekman

* Github: https://github.com/mtekman

* ORCID: https://orcid.org/0000-0002-4181-2676

* Google Scholar: https://scholar.google.com/citations?hl=en&user=HVwU31YAAAAJ

* LinkedIn: https://www.linkedin.com/in/mehmet-tekman-4a08b484/

Contact: @mtekman:matrix.org or mtekman89@gmail.com

meet.hn/city/gb-London

Socials: - github.com/mtekman - linkedin.com/in/https://www.linkedin.com/in/mehmet-tekman-4a08b484/ - mtekman.at.hn

Interests: Science, Web Development, Programming, Data Science, AI/ML, Gaming, Hacking, Hardware, Mobile Development, Open Source, Research, Biotech

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submissionscomments
mtekman··on parrot.live
Reminds me of smithers.el

https://gitlab.com/mtekman/smithers.el/

mtekman··on Ask HN: Who wants to be hired? (July 2024)

    Name: Mehmet
    Location: UK or Germany
    Work Preferences: Remote/Hybrid/Office
    Technologies: R, Python, Javascript, C++, Common Lisp
    Resume, CV, Contact: (see my bio)
Several postdocs in bioinformatics, familiar with many different bioinformatic pipelines, tons of teaching and workshop hosting experience, work well as liaison between informaticians and biologists/medics, full stack dev who has empowered many research groups with their own in-house analytical platforms and trained them in its use.

Too long? GNU-obsessed Data Analyst with matrix management skills and a strong focus on reproducible environments and teaching what he knows to others.

mtekman··on Of Psion and Symbian
I got to meet David Potter and his journalist wife when I was working at the Royal Free Hospital. He funded the Potter Chair position which my prof Dr Kleta filled as a nephrologist for many years. I have a picture of myself holding a Nokia N900 and shaking his hand.

At the time I thought he was the reason that the phone existed at all, not quite knowing the delicate politics between Symbian and Maemo at the time.

Still he smiled amicably enough and it's a treasured photo of mine.

mtekman··on RuneLite – open-source RuneScape Client
A lifetime ago I wrote an OpenCV blob detection auto-mining tool for it:

https://gitlab.com/mtekman/runescape-motiondetector

It worked for about an hour before having the nasty habit of attacking monsters, chasing them out into the wilderness where you'd check in on your character and find him dead, barren, and lost.

Fun though.

mtekman··on What You Get After Running an SSH Honeypot for 30 Days
I used to run fail2ban, but I found it (or at least its defaults) ineffective against discouraging further requests. With iptables, you can specify the connection to hang for a period and then drop
mtekman··on What You Get After Running an SSH Honeypot for 30 Days
I have a utility that parses ssh failed attempts and creates iptables blocklists:

https://gitlab.com/mtekman/iptables-autobanner

For those just wanting the blocklist, here is a table of malicious IP addresses, with columns of: address, number of ports tried, number of usernames tried.

https://upaste.de/bgC

mtekman··on Ask HN: Who wants to be hired? (June 2024)

    Name: Mehmet
    Location: UK or Germany
    Work Preferences: Remote/Hybrid/Office
    Technologies: R, Python, Javascript, C++, Common Lisp
    Resume, CV, Contact: (see my bio)
Several postdocs in bioinformatics, familiar with many different bioinformatic pipelines, tons of teaching and workshop hosting experience, work well as liaison between informaticians and biologists/medics, full stack dev who has empowered many research groups with their own in-house analytical platforms and trained them in its use.

Too long? GNU-obsessed Data Analyst with matrix management skills and a strong focus on reproducible environments and teaching what he knows to others.

mtekman··on A smooth and sharp image interpolation you probably haven't heard of
probably because the visual differences are so slight that there is no benefit in showing them to someone who isn't deeply entrenched in the topic
mtekman··on Ask HN: Who wants to be hired? (May 2024)

    Name: Mehmet
    Location: UK or Germany
    Work Preferences: Remote/Hybrid/Office
    Technologies: R, Python, Javascript, C++, Common Lisp
    Resume, CV, Contact: (see my bio)
     
Several postdocs in bioinformatics, familiar with many different bioinformatic pipelines, tons of teaching and workshop hosting experience, work well as liaison between informaticians and biologists/medics, full stack dev who has empowered many research groups with their own in-house analytical platforms and trained them in its use.

Too long? GNU-obsessed Data Analyst with matrix management skills and a strong focus on reproducible environments and teaching what he knows to others.

mtekman··on Visualizing malicious IP addresses
I use the same pattern for my iptables banner.

It's essentially a manual firewall for when I disable ufw if it's being too aggressive:

https://gitlab.com/mtekman/iptables-autobanner

mtekman··on Looking into an apparently scammy looking zsh plugin manager called “zi”
Same for these "lightning fast" bashrc frameworks. I boiled down my main cases into 15 lines in my rc:

https://mstdn.science/@mtekman/111861830339082890

mtekman··on Ask HN: Who is hiring? (April 2024)
Hah, no worries - if ever you start anything in the UK/EU space, feel free to ping me!
mtekman··on Ask HN: Who is hiring? (April 2024)
Ah. This would be perfect for me (see my bio), but I'm only UK and EU based. I'd do remote if I could.
mtekman··on Why Pandas feels clunky when coming from R
because the vector contains characters, so clearly it encodes categorical data and not numeric
mtekman··on Why Pandas feels clunky when coming from R
There's also this new Gem:

https://mstdn.science/@mtekman/111964030735312859

mtekman··on Ask HN: Who wants to be hired? (February 2024)

    Name: Mehmet
    Location: UK or Germany
    Work Preferences: Remote/Hybrid/Office
    Technologies: R, Python, Javascript, C++, Common Lisp
    Resume, CV, Contact: (see my bio)
     
Several postdocs in bioinformatics, familiar with many different bioinformatic pipelines, tons of teaching and workshop hosting experience, work well as liaison between informaticians and biologists/medics, full stack dev who has empowered many research groups with their own in-house analytical platforms and trained them in its use.

Too long? GNU-obsessed Data Analyst with a strong focus on reproducible environments and teaching what he knows to others.

mtekman··on Simulating a minimal cell in the browser
This is really amazing. I wonder if confounders such as transcriptional bursting[1] are modelled too? I did not check but I assume cell-cycle is readily modelled.

1: The tendency of a single cell to perform transcription in bursts of activity/inactivity, which averages in bulk tissue as a continuous variable.

mtekman··on Feynman: I am burned out and I'll never accomplish anything (1985)
Thanks for the insight!
mtekman··on Feynman: I am burned out and I'll never accomplish anything (1985)
> I started interviewing for positions in (tech) industry, got a monetary offer 5 times what I was making as a senior postdoc, started a new career, and never looked back.

Hello, I'm in a similar sort of transition position. May I ask where you applied (US/UK/EU-based?) and what your main experience was in adapting your academic CV to industry?

(Feel free to reach me by email or matrix too)

mtekman··on Something special is happening in Barcelona
Cyclists are still given the stink eye in England if they even consider cycling on the pavement (I was once physically assaulted as a teen by a 'concerned citizen' for doing such a reckless thing), despite it being completely normal in other European cities.

Before the bike lanes were common, you had to cut your teeth zipping between the cars in the narrow roads, keeping up with traffic speeds, annoying every driver who gave you an inch, terrifying bewildered tourists, and watching your face get smashed by door after door after door.

When the cycle lanes were rolled out, things became much safer between bikes and cars, but now all bikes are herded together and you experience a bike lane traffic as Mr Expensive Latex seems to have no idea how to pull over to let others pass whilst he's busy clicking in his shoes.

It's very safe now. I kind of miss the mad chaos London used to be when cycling, when only the dumb and the brave dared to battle the busses. When you'd get to work pumped with the adrenaline and the knowledge that you survived the journey

mtekman··on IPv4 vs. IPv6 FAQ
For anyone wondering why they cant access their ipv6-addressed pi box from public WiFi networks: those public networks still use ipv4 and assign you only a lonk-local ipv6 address.

To go from 4 to 6, the public WiFi box will need to use a 4 to 6 "broker" and there are surprisingly few of these around and they're not usually free.

So basically, your home network and Pi is future-ready, but public infrastructure might need a moment...

mtekman··on 20 Years of Haiku
Its a very opinionated OS, like iOS/Windows (but freer in every sense), where there is usually only one way to do something.

No choice of desktop managers or window managers, just very lean and streamlined software with little redundancy

I think people like it because its neat.

mtekman··on Climate change: IPCC report is 'code red for humanity'
Emissions from aviation contributes 3% to greenhouse gasses.
mtekman··on New in Git: switch and restore
In a similar manner for Emacs users: magit-toggle-refine-hunk is a lifesaver for word diffs
mtekman··on When ejecting from a helicopter, the rotor blades are jettisoned
I can't help but imagine jettisoned rotors falling to the ground like spiraling beams and wedging themselves a good portion into the earth like throwing a knife into the ground
mtekman··on Amazon Kindles with 3G will start to lose cellular network access in December
I'm actually working on a project to revive Amazon Kindles as personal productivity devices. I'm very close to release, and will open the source soon
mtekman··on How Dwarf Fortress is built
One of the brothers is the main developer and ideas guy, the other is more the admin/idea control/art role